Contacts of the helix formed by residues 140 - 167 (chain A) in PDB entry 3URZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 4.0 15.4 - - - +
108A ASP* 5.2 2.2 + - - -
111A GLU* 4.8 3.3 + - - +
133A ILE* 3.2 26.3 - - + +
134A LEU* 4.7 0.9 - - + -
137A GLU* 3.1 44.3 + - + +
138A ALA 3.4 3.6 + - - -
139A ASP* 1.3 72.4 - - - +
141A LEU* 1.3 65.0 + - - +
142A ALA* 3.6 11.6 + - - +
143A ALA* 3.2 26.7 + - + -
144A ASN* 2.7 30.5 + - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 3.2 7.2 + - - +
140A ASN* 1.3 76.1 - - - +
142A ALA* 1.3 64.2 + - - +
144A ASN* 3.9 3.1 - - - +
145A ILE* 3.1 40.2 + - + +
201A LYS 4.7 3.8 - - - +
202A VAL* 3.7 43.3 - - + +
206A PHE* 4.1 31.4 - - + -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.2 44.2 - - + +
115A GLU* 5.7 0.4 - - - +
130A TYR* 4.5 4.8 - - + -
133A ILE* 5.9 0.2 - - + -
140A ASN* 3.5 8.5 + - - +
141A LEU* 1.3 78.3 - - - +
143A ALA* 1.3 62.9 + - - +
145A ILE* 3.4 11.0 + - - +
146A PHE* 3.3 21.5 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 3.7 30.0 - - + +
133A ILE* 3.7 26.0 - - + +
134A LEU* 3.7 21.8 - - + -
140A ASN* 3.2 6.0 + - + +
142A ALA* 1.3 77.7 - - - +
144A ASN* 1.3 58.1 + - - +
146A PHE* 3.5 1.6 + - - +
147A LEU* 3.1 35.9 + - - +
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Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.2 19.1 - - - +
138A ALA 3.2 22.0 + - - +
139A ASP* 3.4 11.1 - - - +
140A ASN 2.7 23.6 + - - +
141A LEU* 4.0 2.0 - - - +
143A ALA* 1.3 74.4 - - - +
145A ILE* 1.3 62.8 + - - +
147A LEU* 4.9 0.2 - - - -
148A GLY* 3.1 18.4 + - - -
198A SER* 3.3 44.0 + - - +
199A LEU* 4.9 0.3 - - - +
201A LYS* 3.9 17.3 + - + +
202A VAL* 3.8 13.9 - - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.1 42.1 + - + +
142A ALA* 3.7 8.3 - - - +
143A ALA 3.3 0.4 - - - -
144A ASN* 1.3 75.5 - - - +
146A PHE* 1.3 65.9 + - - +
148A GLY* 4.0 0.3 - - - -
149A ASN* 3.2 44.2 + - - +
199A LEU* 5.1 2.8 - - + +
202A VAL* 3.8 26.0 - - + -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 3.7 40.4 - - + -
123A GLU* 6.5 0.4 - - + -
126A ALA* 5.5 0.7 - - + -
127A LEU* 4.7 8.5 - - + -
130A TYR* 3.4 48.5 - + + +
142A ALA 3.3 8.3 + - - +
143A ALA 3.9 5.4 - - - +
145A ILE* 1.3 82.7 - - - +
147A LEU* 1.3 71.3 + - + +
149A ASN* 3.4 5.0 + - - +
150A TYR* 2.8 54.6 + + + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.6 33.4 - - + +
130A TYR* 4.1 25.1 - - + +
131A GLU* 4.5 5.2 - - + +
134A LEU* 3.3 35.2 - - + -
143A ALA 3.1 17.7 + - - +
146A PHE* 1.3 87.1 - - + +
148A GLY* 1.3 59.7 + - - +
150A TYR* 3.9 3.4 - - + -
151A TYR* 2.9 59.7 + - + +
198A SER* 4.2 9.9 - - - +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASN 3.1 20.0 + - - -
145A ILE 4.0 0.7 - - - -
147A LEU* 1.3 75.5 - - - +
149A ASN* 1.3 63.4 + - - +
152A TYR* 3.4 23.2 + - - +
195A ALA* 3.5 27.2 - - - +
198A SER* 3.7 6.1 - - - -
199A LEU* 3.9 12.7 - - - +
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Residues in contact with ASN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.2 33.4 + - - +
146A PHE* 3.8 4.4 - - - +
148A GLY* 1.3 76.0 - - - +
150A TYR* 1.3 59.4 + - - +
151A TYR 3.5 0.2 - - - -
152A TYR* 4.0 5.6 - - - +
153A LEU* 3.0 45.7 + - + +
199A LEU* 4.0 14.4 - - - +
210A GLU* 5.6 11.8 + - - +
214A THR* 5.0 7.4 + - - +
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.1 39.7 + - + +
127A LEU* 3.6 37.4 - - + +
146A PHE* 2.8 43.4 + + + +
147A LEU* 3.2 8.7 + - - +
149A ASN* 1.3 76.0 - - - +
151A TYR* 1.3 77.3 + + - +
153A LEU* 4.1 3.2 - - - +
154A THR* 2.7 55.8 + - + +
191A ARG* 4.3 11.1 + - - -
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.5 14.6 - - + +
131A GLU* 5.5 6.4 + - - -
147A LEU* 2.9 51.1 + - + +
150A TYR* 1.3 90.1 - + - +
152A TYR* 1.3 59.1 + - - +
154A THR* 3.2 3.2 + - - -
155A ALA* 2.9 33.1 + - - +
191A ARG* 3.4 51.5 - - + +
194A LYS* 3.9 42.1 + - + +
195A ALA* 3.8 9.6 - - + +
198A SER* 5.6 0.4 - - - -
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY 3.4 19.7 + - - +
149A ASN* 4.0 5.8 - - - +
150A TYR 3.4 0.4 - - - -
151A TYR* 1.3 77.9 - - - +
153A LEU* 1.3 75.0 - - + +
155A ALA* 3.9 3.9 - - - +
156A GLU* 3.1 47.1 + - + +
192A TYR* 3.8 21.4 + + - -
195A ALA* 3.6 9.5 - - + +
214A THR* 3.7 24.7 - - + -
217A LYS* 3.2 47.5 + - + +
218A ILE* 3.7 29.2 - - + -
221A ILE* 4.8 3.4 - - + +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN* 3.0 30.0 + - + +
150A TYR* 4.2 3.6 - - - +
152A TYR* 1.3 90.2 - - + +
154A THR* 1.3 65.0 + - + +
156A GLU* 3.4 10.1 + - + +
157A GLN* 3.4 23.6 + - - +
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Residues in contact with THR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU* 5.1 3.4 - - - +
150A TYR* 2.7 50.4 + - + +
151A TYR* 3.2 8.5 + - - -
153A LEU* 1.3 76.7 - - + +
155A ALA* 1.3 58.2 + - - +
157A GLN* 3.2 37.2 + - - +
158A GLU* 3.3 17.2 - - - +
191A ARG* 2.9 30.8 + - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR 2.9 20.6 + - - +
152A TYR 3.9 2.0 - - - +
154A THR* 1.3 74.5 + - - +
156A GLU* 1.3 60.1 + - - +
157A GLN 3.4 0.2 - - - -
158A GLU* 3.5 1.5 + - - -
159A LYS* 3.0 28.8 + - - +
187A LEU* 3.4 18.6 - - + +
191A ARG* 3.4 17.5 - - + +
192A TYR* 3.4 32.6 + - + +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.1 37.5 + - + +
153A LEU* 3.5 13.0 - - + +
154A THR 3.3 0.2 - - - -
155A ALA* 1.3 77.4 - - - +
157A GLN* 1.3 60.2 + - - +
159A LYS* 3.3 12.1 + - - +
160A LYS* 3.2 21.1 + - - +
192A TYR* 2.9 23.6 + - - -
221A ILE* 3.7 14.3 - - - +
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU 3.4 8.9 + - - +
154A THR* 3.2 41.0 + - - +
156A GLU* 1.3 74.9 - - - +
158A GLU* 1.3 63.6 + - + +
160A LYS* 3.4 9.4 + - - +
161A LYS* 3.1 26.7 + - - +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.3 18.5 + - - +
155A ALA 3.8 4.7 - - - +
156A GLU 3.4 0.4 - - - -
157A GLN* 1.3 79.2 - - + +
159A LYS* 1.3 60.2 + - - +
161A LYS* 3.5 21.5 + - - +
162A LEU* 3.1 28.6 + - - +
187A LEU* 3.9 27.4 - - + -
191A ARG* 5.0 6.6 + - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA 3.0 17.5 + - - +
156A GLU* 3.5 14.2 + - - +
157A GLN 3.3 0.2 - - - -
158A GLU* 1.3 76.3 - - - +
160A LYS* 1.3 61.0 + - - +
162A LEU* 3.6 8.0 + - - +
163A GLU* 2.8 53.2 + - - +
184A LEU* 4.0 20.6 - - + -
187A LEU* 5.0 5.3 - - + +
192A TYR* 3.5 22.4 - - + +
221A ILE* 3.6 34.3 - - + +
224A GLU* 4.8 11.3 + - - -
225A VAL* 5.3 3.1 - - - -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU 3.2 13.2 + - - +
157A GLN* 3.7 11.9 - - - +
158A GLU 3.3 0.2 - - - -
159A LYS* 1.3 74.2 - - - +
161A LYS* 1.3 55.9 + - - +
163A GLU* 3.4 9.7 + - - +
164A THR* 2.7 45.3 + - - +
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLN 3.1 16.1 + - - +
158A GLU* 3.7 23.1 - - - +
159A LYS 3.4 0.2 - - - -
160A LYS* 1.3 75.4 - - - +
162A LEU* 1.3 62.0 + - - +
164A THR* 3.9 5.2 - - - -
165A ASP* 3.0 49.8 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU 3.1 18.4 + - - +
159A LYS* 3.7 6.5 - - - +
161A LYS* 1.3 78.7 - - - +
163A GLU* 1.3 59.5 + - - +
165A ASP* 3.8 6.3 + - + +
166A TYR* 3.6 13.3 + - - +
179A ARG 4.6 2.0 - - - +
180A TYR* 3.5 42.0 - - + +
183A GLY* 3.4 14.4 - - - +
184A LEU* 3.2 48.9 - - + +
187A LEU* 5.7 2.9 - - + -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LYS* 2.8 53.2 + - + +
160A LYS* 3.4 7.9 + - - +
162A LEU* 1.3 75.1 - - - +
164A THR* 1.3 60.3 + - - +
167A LYS* 3.0 57.8 + - - +
180A TYR* 3.6 32.1 + - + +
184A LEU* 4.6 4.7 - - + +
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 2.7 33.5 + - - +
161A LYS* 3.9 7.1 - - - -
162A LEU 3.5 0.2 - - - -
163A GLU* 1.3 76.8 - - - +
165A ASP* 1.3 64.9 + - - +
167A LYS* 4.0 14.0 - - - +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 3.0 40.9 + - - +
162A LEU* 4.0 7.1 - - + +
163A GLU 3.3 0.2 - - - -
164A THR* 1.3 82.2 - - - +
166A TYR* 1.3 62.8 + - - +
167A LYS 4.8 0.9 - - - -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU 3.6 5.3 + - - +
163A GLU 4.2 1.8 - - - +
164A THR 3.5 0.2 - - - -
165A ASP* 1.3 80.1 - - - +
167A LYS* 1.3 67.6 + - + +
172A PRO* 4.8 14.7 - - + +
176A GLN 5.6 2.0 - - - +
177A TYR* 6.2 1.8 - - + -
180A TYR* 3.8 42.2 - - + -
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU* 3.0 45.7 + - - +
164A THR* 4.0 16.2 - - - +
165A ASP 4.8 0.9 - - - -
166A TYR* 1.3 83.1 - - + +
180A TYR* 5.2 8.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il